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(-) Description

Title :  STRUCTURE OF PSEUDOMONAS FLUORESCENCE LAPD EAL DOMAIN COMPLEXED WITH C-DI-GMP, P6522
 
Authors :  H. Sondermann, M. V. A. S. Navarro, P. Krasteva
Date :  10 Nov 10  (Deposition) - 09 Feb 11  (Release) - 23 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tim Barrel, C-Di-Gmp Receptor, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. V. Navarro, P. D. Newell, P. V. Krasteva, D. Chatterjee, D. R. Madden G. A. O'Toole, H. Sondermann
Structural Basis For C-Di-Gmp-Mediated Inside-Out Signaling Controlling Periplasmic Proteolysis.
Plos Biol. V. 9 E1000 2011
PubMed-ID: 21304926  |  Reference-DOI: 10.1371/JOURNAL.PBIO.1000588

(-) Compounds

Molecule 1 - CYCLIC DIMERIC GMP BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 400-648
    Gene: LAPD, PFL01_0131
    Organism Scientific: PSEUDOMONAS FLUORESCENS
    Organism Taxid: 205922
    Strain: PF0-1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1C2E1Ligand/Ion9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1C2E2Ligand/Ion9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:1 , HOH A:2 , HOH A:31 , HOH A:61 , HOH A:62 , HOH A:77 , GLN A:431 , LYS A:446 , LEU A:448 , SER A:449 , ARG A:450 , PRO A:460 , ALA A:461 , GLY A:462 , LEU A:465 , ASP A:478 , MET A:481 , ASN A:499 , GLN A:560 , ARG A:561 , ARG A:618 , VAL A:619 , GLU A:620 , GLY A:638 , GLN A:639 , PRO A:644 , HOH A:663 , HOH A:673BINDING SITE FOR RESIDUE C2E A 2256

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PJU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PJU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PJU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PJU)

(-) Exons   (0, 0)

(no "Exon" information available for 3PJU)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:249
 aligned with Q3KK31_PSEPF | Q3KK31 from UniProtKB/TrEMBL  Length:648

    Alignment length:249
                                   409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639         
         Q3KK31_PSEPF   400 QSLVADVGDDHHAWHRLLDQALNQRRFELFFQPVVAAQDTQLVLHYKVLSRLLDEQGQTIPAGRFLPWLERFGWTARLDRLMLERVLEQMAGHEESLALNLSSATLADPQALNKVFEILRAHSNLGARLTLEIGEEQLPEQAVLEQLTRRLRELGFSLSLQRFGGRFSMIGNLARLGLAYLKIDGSYIRAIDQESDKRLFIEAIQRAAHSIDLPLIAERVETEGELSVIREMGLYGVQGQLFGEPKPWG 648
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------EAL-3pjuA01 A:414-644                                                                                                                                                                                                                  ---- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhh..eeeeeeeeee......eeeeeeeeeee.....eeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhh.hhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhh......eee.hhhh.hhhhhhhhhhhhhhhhhhhhhh...eee....hhhhhhhhhhh...ee.hhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pju A 400 QSLVADVGDDHHAWHRLLDQALNQRRFELFFQPVVAAQDTQLVLHYKVLSRLLDEQGQTIPAGRFLPWLERFGWTARLDRLMLERVLEQMAGHEESLALNLSSATLADPQALNKVFEILRAHSNLGARLTLEIGEEQLPEQAVLEQLTRRLRELGFSLSLQRFGGRFSMIGNLARLGLAYLKIDGSYIRAIDQESDKRLFIEAIQRAAHSIDLPLIAERVETEGELSVIREMGLYGVQGQLFGEPKPWG 648
                                   409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3PJU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PJU)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: EAL] (10)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q3KK31_PSEPF | Q3KK31)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q3KK31_PSEPF | Q3KK31: 3pjt 3pjv 3pjw 3pjx

(-) Related Entries Specified in the PDB File

3pjt 3pjv 3pjw 3pjx